Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
-
Full-text index only
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.
PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups
A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome
-
Full-text index only
With the finished human genome in hand, what next?
PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups
Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.
-
Full-text index only
Variation resources at UC Santa Cruz.
PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups
The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.
-
Full-text index only
EGASP: Introduction.
PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups
Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.
-
Full-text index only
Kinetoplastid genomics: the thin end of the wedge.
PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups
Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.
-
Full-text index only
Comparative genomic analysis of three Leishmania species that cause diverse human disease.
PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups
L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species
-
Full-text index only
Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.
PMID 19689818 · PMC2743709 · BMC cancer · 2009 · 7 claims · 3 setups
The previously reported classifier (m/z 8,132 and 4,002) failed to discriminate CRC patients from healthy volunteers in this independent validation cohort
-
Full-text index only
Efficacy assessment of SNP sets for genome-wide disease association studies.
PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups
τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP
-
Full-text index only
Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.
PMID 18984079 · PMC2679897 · American journal of obstetrics and gynecology · 2008 · 8 claims · 7 setups
Women with severe preeclampsia present a unique urinary proteomic fingerprint distinguishable from controls.
-
Full-text index only
SysZNF: the C2H2 zinc finger gene database.
PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups
SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links
-
Full-text index only
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.
PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups
A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)
-
Full-text index only
From single cells to whole organisms.
PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups
The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods
-
Full-text index only
Proteomics and genomics: perspectives on drug and target discovery.
PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups
Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma
-
Full-text index only
The UCSC Genome Browser Database: 2008 update.
PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.
-
Full-text index only
Genomics--from Neanderthals to high-throughput sequencing.
PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups
Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.